Step 1: Delete the Old Version
1.1. In the admin dashboard go to Appearance > Themes.
1.2. Deactivate the Old Version: need activate the theme by default, for example Twenty Sixteen.
1.3. Hover mouse on the target theme, click Theme Details link.
1.4. In the lower right corner of the theme window click Delete.

Step 2: Upload the New Version
2.1. After deleting the old version of the target theme, upload the newer package with latest version of the target theme.
2.2. Now you can activate the latest version of the target theme.

Note: Updating a theme maybe will reset the customize you’ve made in the previous version.